FSI Flashcards
octamer of histones + spiral/solenoid stability
h2a, h2b, h3 and h4
h1 binds nucleosome and linker DNA. may stabilize spiral/solenoid stuff through interaction with histone N terminal tails
where does HAT acetylate and how does it work
transfer acetyl to NH3+ group of lysine
removes the + charge on histones, decreasing strong interaction with - PO4 dna groups
“writer”
general transcription factors
locate tata, define start of transcription, recruit rna pol 2, low rate of transcription with no specificity, present in all cell nuclei
proximal promoter, consensus sequence
tata box
- meaning that it is found in a lot of things
- close to a promoter region
- binds specific transcription factors (tissue spec)
- approx 18-26 bases upstream
timing of transcription initiation specific factors
chromatin remodelling, histone mod, TBP finds tata, then TF2D, then B, E, H (general transcription factors that guide pol 2). guide the formation of the basal transcription complex
regulatory transcription factors
control rate of transcription, function as activators or repressors, often tissue specific
transcription process
tata box recognition, activation/dna binding/dimerization, a helix binds to groove bending dna and separating strands, basic/hydrophobic AA (leu) stabilize DNA binding
zinc finger motif transcription factor
zinc finger binds to specific motifs like 2 cys/2 his
- activation by ligands like hormones binding to receptor
- binds in major groove and forms a stretch of a helices
- zinc holds a helix and b sheet together. cluster of 3 that form in major groove and have a helix to connect. strong and specific
When it needs to open the DNA sequence, it needs tighter binding so you need more than one protein to accomplish this
dna binding domain in transcription factor
recognizes consensus dna sequence
-a helix with basic aa, lies in major or minor groove and contacts n bases (DIRECTLY), basic aa stabilize binding
- bend dna!
activation domain in transcription factor
interacts with other tx factors
domains of transcription factors
activation, dna binding, dimerization (from N to C terminus)
bzip
DNA binding: each subunit has 1 a helix. a helices with basic aa that contact n bases in major groove. basic aa stabilize them
dimerization: amphipathic a helix. dimerizes in coiled coil by hydrophobic interactions
ex. leucine zipper
leucine zipper dimerization domain
every 7th aa is leucine. heptad repeat
provides amphipathic a helix for dimerization
- other hydrophobic aa could replace leu
ap1 transcription factor
activator protein 1
- bzip protein!
- ubiquitous tx factor
- regulates gene expression in response to growth factors, stress, pathogens
- controls cell processes including differentiation and cell division
- activation domain interacts with other tfs
nuclear receptor family dimer proteins
- must be acticated by ligand binding (lipid sol hormones and vitamins)
- coordinate the response of many genes to a hormone signal
- enter by active diffusion and bind to intracell receptors
- receptors are conserved!
dna binding domain of GR
nuclear receptor family
- each subunit has 2 zinc fingers
- 1 a helix of 1 zinc finger lies in major grooce and binds to similar sequence in dna. thus its 2 half sites
- there’s a lever arm that moves
can activate many genes at once as long as they have the GRE
myogenesis
done by myoD, myf5 and myogenin
- HLH protein
- binds reg region in many muscle specific genes, conserved
bone formation
runx2
- binds to enhancers
- runt domain clamps the dna between c terminal tail in major groove and the wing in minor groove
- mutation is cleidocranial dysplasia
MRNA cap
xtra nuc added to 5’ end. 7 methyl guanosine. added by 5’ to 5’ tiphosphate bond
- added as primary transcript emerges (not encoded)
- increases stability and required for translation
- polio target, makes itself without CBP!
intron removal and ligation esterification
2 transesterification reactions
- 2’ OH of one site attacks the 5’ splice site
- 2’ OH is attached to 5’ site
3’ OH upstream attacks 3’ splice site
exons joined by ligation
intron removal, protein side
large RNP with small nuclear RNP that have specific small nuclear RNA that are complementary to consensus sequences in precursor rna
- help in poitioning the spliceosome on precursor rna
binding
- at 5’ end and branch point. then form spliceosome then 5’ site is cleaved, 3’ is cleaved
poly A tail
protien binds AAUAAA
- cleavage factors CFI and CFII cleave rna
- poly A polymerase adds poly A posttranscriptionally
- increases stability and translational efficiency
miRNA processing
transcribed by pol 2 or intron derived
- regulate post transcriptionally
- each mrna has many target sequences for miRNA
- first forms pri-mirna from pol 2 or intron by forming hairpin structure
- processed by drosha in nuc forming pre-miRNA
- dicer cuts it in cyto
one strand is selected, other is degraded. assemble them into microRNPS or miRISC (from argonaute family)
- reg dna expression by destabilizing mrna or interfering with translation
moving from transcription to translation in cyto
cap binding protein.
mRNA then associates with cap and poly a binding proteins to form mRNPs (aka exon junction complex). mRNPS are transported thru nuclear pore from 5’ end then the cap is removed and eIF4 initiation factor is added